calibre does not compress files, it does not store all books in one file, it is perfectly possible to do differential backups with calibre's library (I do it all the time). You can change where calibre stores its books, in fact you can have multiple libraries at different locations. You can run calibre entirely off a USB key if you want to.

The OP really should ask about things before making assumptions and then complaining.

Well actually the OP only complained about the folder layout. Pepak later came in and complained about the backup issue.